refseq-methods: Retrieve reference sequences ('XStringSet'-class) from...

In phyloseq: Handling and analysis of high-throughput microbiome census data

Description

This is the suggested method for accessing the phylogenetic tree, (XStringSet-class) from a phyloseq data object (phyloseq-class). Like other accessors (see See Also, below), the default behavior of this method is to stop with an error if physeq is a phyloseq-class but does not contain reference sequences (the component data type you are trying to access in this case).

Usage

refseq(physeq, errorIfNULL=TRUE)

## S4 method for signature 'ANY'
refseq(physeq, errorIfNULL = TRUE)

## S4 method for signature 'XStringSet'
refseq(physeq)

Arguments

physeq	(Required). An instance of phyloseq-class that contains a phylogenetic tree. If physeq is a phylogenetic tree (a component data class), then it is returned as-is.
errorIfNULL	(Optional). Logical. Should the accessor stop with an error if the slot is empty (NULL)? Default TRUE.

Value

The phylo-class object contained within physeq; or NULL if physeq does not have a tree. This method stops with an error in the latter NULL case be default, which can be over-ridden by changing the value of errorIfNULL to FALSE.

See Also

otu_table, sample_data, tax_table phy_tree, phyloseq, merge_phyloseq

Examples

 data(GlobalPatterns)
 refseq(GlobalPatterns, FALSE)

Example output

NULL

phyloseq documentation built on Nov. 8, 2020, 6:41 p.m.